>> That leads to:
>>
>> THE SECOND BIG QUESTION
>> -----------------------
>> If we follow these rules, will we ever have a situation where we will
>> automatically create bonds when the end-user did not want one?
>
> Oh yes!! Chime is/was quite happy to connect Al w/ Si in
> aluminosilicates if they came within some (unkowable, unmodifiable)
> distance. And for the benefit of nonchemists and organic chemists, the
> proper bond sequence is -Al-O-Si- , and of course -Si-O-Si- and -Al-O-Al
> in the oxides instead of -Al-Al- and -Si-Si- connected based purely on
> proximity.
Q: Can you use a file format other than .pdb?
Q: Are there external tools that can be used to generate full connectivity
and add CONECT records to .pdb files?
The proposal we are exploring (for .pdb files *only*) is that Jmol
1. apply connectivity from the .pdb file
2. apply auto-bonding *only* for atoms that were not
mentioned in the CONECT records
If the .pdb file contained full connectivity information, all CONECT
records are specified, then I think there is only one case where algorithm
would fail:
- two singleton atoms
- each of them not bonded to anything
- but close enough to each other to bond
- the auto-bonder would establish a bond where one was not intended
Can anything like this happen in a real file? Even one which is
intentionally wacky?
Miguel
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